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(-) Description

Title :  CRYSTAL STRUCTURE OF SEQA BOUND TO DNA
 
Authors :  Y. S. Chung, T. Brendler, S. Austin, A. Guarne
Date :  22 Dec 08  (Deposition) - 28 Apr 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Protein-Dna Complex, Hemimethylated Gatc, Dna Replication, Sequestration, Dna Replication Inhibitor, Dna-Binding, Replication Inhibitor/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. S. Chung, T. Brendler, S. Austin, A. Guarne
Structural Insights Into The Cooperative Binding Of Seqa To A Tandem Gatc Repeat
Nucleic Acids Res. V. 37 3143 2009
PubMed-ID: 19304745  |  Reference-DOI: 10.1093/NAR/GKP151
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN SEQA
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQADELTA(41-59)
    Gene: B0687, JW0674, SEQA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
 
Molecule 2 - 5'-D(*GP*AP*GP*TP*CP*GP*(6MA) P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'
    Chains: C, G
    Engineered: YES
    Other Details: METHYLATED OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - 5'- D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP *GP*AP*C)-3'
    Chains: D, H
    Engineered: YES
    Other Details: UNMETHYLATED OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
16MA4Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
16MA2Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
16MA2Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:76 , THR E:180BINDING SITE FOR RESIDUE MPD E 182
2AC2SOFTWARETHR A:180 , LEU F:76BINDING SITE FOR RESIDUE MPD A 182
3AC3SOFTWAREARG A:30 , LYS A:34 , GLU B:9 , TYR B:13BINDING SITE FOR RESIDUE MPD A 183
4AC4SOFTWAREARG E:30 , LYS E:34 , GLU F:9 , TYR F:13BINDING SITE FOR RESIDUE MPD E 183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FMT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FMT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FMT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FMT)

(-) Exons   (0, 0)

(no "Exon" information available for 3FMT)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:162
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_ECOLI     1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKFSAASQPAAPVTKEVRVASPAIVEAKPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhh.-------------------....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh....eee......eee...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmt A   1 MKTIEVDDELYSYIASHTKHIGESRSDILRRMLKFSAASQ-------------------KPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    10        20        30        40         -        60        70        80        90       100       110       120       130       140       150       160       170       180 
                                                                  40                  60                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_ECOLI     1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKFSAASQPAAPVTKEVRVASPAIVEAKPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhh......hhhhhhhhhhh.------------------------....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh....eee......eee...hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmt B   1 MKTIEVDDELYSYIASHTKHIGESRSDILRRMLKF------------------------KPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    10        20        30    |    -         -        60        70        80        90       100       110       120       130       140       150       160       170       180 
                                                             35                       60                                                                                                                         


Chain C from PDB  Type:DNA  Length:22
                                                      
                 3fmt C   1 GAGTCGaTCGGCGGGaTCCTTA  22
                                  | 10     |  20  
                                  7-6MA   16-6MA  


Chain D from PDB  Type:DNA  Length:21
                                                     
                 3fmt D   1 TTAAGGATCCCGCCGATCGAC  22
                            ||      11        21 
                            1|                   
                             3                   


Chain E from PDB  Type:PROTEIN  Length:162
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_ECOLI     1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKFSAASQPAAPVTKEVRVASPAIVEAKPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fmtE01 E:1-60 Met repressor-like                          3fmtE02 E:60-181 Replication modulator SeqA, C-terminal DNA-binding domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhh.-------------------....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh....eee......eee...hhhhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmt E   1 MKTIEVDDELYSYIASHTKHIGESRSDILRRMLKFSAASQ-------------------KPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    10        20        30        40         -        60        70        80        90       100       110       120       130       140       150       160       170       180 
                                                                  40                  60                                                                                                                         


Chain F from PDB  Type:PROTEIN  Length:157
 aligned with SEQA_ECOLI | P0AFY8 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           SEQA_ECOLI     1 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKFSAASQPAAPVTKEVRVASPAIVEAKPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhh......hhhhhhhhhhh.------------------------....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhhhhhh....eee......eee...hhhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmt F   1 MKTIEVDDELYSYIASHTKHIGESRSDILRRMLKF------------------------KPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI 181
                                    10        20        30    |    -         -        60        70        80        90       100       110       120       130       140       150       160       170       180 
                                                             35                       60                                                                                                                         


Chain G from PDB  Type:DNA  Length:22
                                                      
                 3fmt G   1 GAGTCGaTCGGCGGGaTCCTTA  22
                                  | 10     |  20  
                                  7-6MA   16-6MA  


Chain H from PDB  Type:DNA  Length:21
                                                     
                 3fmt H   1 TTAAGGATCCCGCCGATCGAC  22
                            ||      11        21 
                            1|                   
                             3
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3FMT)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FMT)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,E,F   (SEQA_ECOLI | P0AFY8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0010385    double-stranded methylated DNA binding    Interacting selectively and non-covalently with double-stranded methylated DNA. Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
    GO:0044729    hemi-methylated DNA-binding    Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0032297    negative regulation of DNA-dependent DNA replication initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication.
    GO:0090143    nucleoid organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleoid. The nucleoid is the region of a bacterial cell, virion, mitochondrion or chloroplast to which the DNA is confined.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:1990097    SeqA-DNA complex    A protein-DNA complex that contains an oligomer of SeqA bound to GATC sites in methylated or newly-synthesized, hemi-methylated double-stranded DNA, with preference for the latter. Binding of SeqA to hemimethylated DNA sequesters oriC, prevents re-methylation of DNA by Dam and in turn stops premature re-initiation of replication during one replication cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SEQA_ECOLI | P0AFY8: 1iu3 1j3e 1lrr 1xrx 2ch3

(-) Related Entries Specified in the PDB File

1iu3 STRUCTURE OF C-TERMINAL DOMAIN OF SEQA BOUND TO A SINGLE HEMIMETHYLATED GATC
1j3e STRUCTURE OF C-TERMINAL DOMAIN OF SEQA BOUND TO A 6MA-G MISMATCH
1lrr STRUCTURE OF C-TERMINAL DOMAIN OF SEQA BOUND TO A SINGLE HEMIMETHYLATED GATC
1xrx STRUCTURE OF OLIGOMERIZATION DOMAIN OF SEQA